--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make_test_data.sh	Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,126 @@
+#!/bin/bash -e
+#
+# List of dependencies
+TOOL_DEPENDENCIES="rnachipintegrator/0.5.0-alpha.7
+ xlsxwriter/0.8.4"
+# Where to find them
+TOOL_DEPENDENCIES_DIR=$(pwd)/test.tool_dependencies.rnachipintegrator
+if [ ! -d $TOOL_DEPENDENCIES_DIR ] ; then
+    echo WARNING $TOOL_DEPENDENCIES_DIR not found >&2
+    echo Creating tool dependencies dir
+    mkdir -p $TOOL_DEPENDENCIES_DIR
+    echo Installing tool dependencies
+    $(dirname $0)/install_tool_deps.sh $TOOL_DEPENDENCIES_DIR
+fi
+# Load dependencies
+for dep in $TOOL_DEPENDENCIES ; do
+    env_file=$TOOL_DEPENDENCIES_DIR/$dep/env.sh
+    if [ -e $env_file ] ; then
+	. $env_file
+    else
+	echo ERROR no env.sh file found for $dep >&2
+	exit 1
+    fi
+done
+#
+# rnachipintegrator_canonical_genes
+#
+# Test #1
+RnaChipIntegrator --name=mm9 \
+		  --cutoff=50000 \
+		  --number=4 \
+		  --xlsx \
+		  --compact \
+		  test-data/mm9_canonical_genes.tsv test-data/mm9_summits.txt
+mv mm9_gene_centric.txt test-data/mm9_summits_per_feature.out
+mv mm9_peak_centric.txt test-data/mm9_features_per_summit.out
+mv mm9.xlsx test-data/mm9_summits.xlsx
+#
+# Test #2
+RnaChipIntegrator --name=mm9 \
+		  --cutoff=50000 \
+		  --number=4 \
+		  --xlsx \
+		  --compact \
+		  test-data/mm9_canonical_genes.tsv test-data/mm9_peaks.txt
+mv mm9_gene_centric.txt test-data/mm9_peaks_per_feature1.out
+mv mm9_peak_centric.txt test-data/mm9_features_per_peak1.out
+mv mm9.xlsx test-data/mm9_peaks1.xlsx
+#
+# Test #3
+RnaChipIntegrator --name=mm9 \
+		  --cutoff=50000 \
+		  --number=4 \
+		  --xlsx \
+		  --summary \
+		  --pad \
+		  test-data/mm9_canonical_genes.tsv test-data/mm9_peaks.txt
+mv mm9_gene_centric.txt test-data/mm9_peaks_per_feature3.out
+mv mm9_peak_centric.txt test-data/mm9_features_per_peak3.out
+mv mm9_gene_centric_summary.txt test-data/mm9_peaks_per_feature3.summary
+mv mm9_peak_centric_summary.txt test-data/mm9_features_per_peak3.summary
+mv mm9.xlsx test-data/mm9_peaks3.xlsx
+#
+# rnachipintegrator_wrapper
+#
+# Test #1
+RnaChipIntegrator --name=test \
+		  --cutoff=130000 \
+		  --number=4 \
+		  --promoter_region=-10000,2500 \
+		  --xlsx \
+		  --compact \
+		  test-data/features.txt test-data/summits.txt
+mv test_gene_centric.txt test-data/summits_per_feature.out
+mv test_peak_centric.txt test-data/features_per_summit.out
+mv test.xlsx test-data/summits.xlsx
+#
+# Test #2
+RnaChipIntegrator --name=test \
+		  --cutoff=130000 \
+		  --number=4 \
+		  --promoter_region=-10000,2500 \
+		  --xlsx \
+		  --compact \
+		  test-data/features.txt test-data/peaks.txt
+mv test_gene_centric.txt test-data/peaks_per_feature1.out
+mv test_peak_centric.txt test-data/features_per_peak1.out
+mv test.xlsx test-data/peaks1.xlsx
+#
+# Test #3
+RnaChipIntegrator --name=test \
+		  --cutoff=130000 \
+		  --number=4 \
+		  --xlsx \
+		  test-data/features.txt test-data/peaks.txt
+mv test_gene_centric.txt test-data/peaks_per_feature2.out
+mv test_peak_centric.txt test-data/features_per_peak2.out
+mv test.xlsx test-data/peaks2.xlsx
+#
+# Test #4
+RnaChipIntegrator --name=test \
+		  --cutoff=130000 \
+		  --number=4 \
+		  --only-DE \
+		  --xlsx \
+		  --compact \
+		  test-data/features.txt test-data/peaks.txt
+mv test_gene_centric.txt test-data/peaks_per_feature3.out
+mv test_peak_centric.txt test-data/features_per_peak3.out
+mv test.xlsx test-data/peaks3.xlsx
+#
+# Test #5
+RnaChipIntegrator --name=test \
+		  --cutoff=130000 \
+		  --number=4 \
+		  --xlsx \
+		  --summary \
+		  --pad \
+		  test-data/features.txt test-data/peaks.txt
+mv test_gene_centric.txt test-data/peaks_per_feature4.out
+mv test_peak_centric.txt test-data/features_per_peak4.out
+mv test_gene_centric_summary.txt test-data/peaks_per_feature4.summary
+mv test_peak_centric_summary.txt test-data/features_per_peak4.summary
+mv test.xlsx test-data/peaks4.xlsx
+##
+#